rs11695034

Variant names:

• chr2-239806946-G-A
• rs11695034
• ENST00000650712.1:n.1915-5233G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650712.1(ENSG00000220256):​n.1915-5233G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,296 control chromosomes in the GnomAD database, including 1,383 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.12 (1383 hom., cov: 33)
• Consequence: ENSG00000220256 ENST00000650712.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210

Genes affected

ENSG00000220256 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000220256	ENST00000650712.1	n.1915-5233G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18905 AN: 152178 Hom.: 1382 Cov.: 33

Gnomad AFR AF: 0.0729

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.0484

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.141

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.124 AC: 18921 AN: 152296 Hom.: 1383 Cov.: 33 AF XY: 0.122 AC XY: 9080 AN XY: 74460

Gnomad4 AFR AF: 0.0729

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.0485

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.141

Alfa AF: 0.149 Hom.: 1343

Bravo AF: 0.121

Asia WGS AF: 0.0870 AC: 301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.55

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11695034; hg19: chr2-240728640;